A prayer room used by Muslim students at New York University was struck by vandals who etched and drew graffiti on the walls and soaked Islamic prayer mats with urine, according to N.Y.U. officials and members of the university’s Muslim community.

The soiled mats and other vandalism were discovered Thursday afternoon in a worship space inside Bobst Library, the university’s towering red building across from Washington Square Park in Greenwich Village.

An image of male genitalia was drawn onto the wall of the room, along with the letters “AEPI,” the nickname of Alpha Epsilon Pi, a nationwide Jewish fraternity that was suspended from N.Y.U. in 2015 for hazing, according to a university directory of suspended fraternities and sororities.

N.Y.U. said it had reported the vandalism to the police and would conduct its own investigation to find and punish the vandals. The university said those found to be responsible would be “subject to the most serious sanctions available through our disciplinary process.”

“This desecration of a religious space is vile, reprehensible and utterly unacceptable,” the university said in a statement on Thursday. “It contravenes every principle of our community, and we condemn it.”

Jonathan Pierce, a spokesman for Alpha Epsilon Pi’s national organization, said it “strongly condemns” the vandalism and would “fully cooperate with the administration’s investigation.”

“We are not aware that any of our members were involved in this disrespectful action,” he said. “Hopefully, the investigation will find the perpetrator and, when they are found, we hope they are punished appropriately by the university.”

The vandalism came amid rising concerns about Islamophobia and antisemitism on college campuses, including N.Y.U.’s, since the start of the war in Gaza in October 2023. The campus conflicts have led to the departures of several university presidents and have driven policy changes since President Trump took office again in January.

The Trump administration has detained international students — many of them Muslim — whom it has vowed to deport because of their involvement in campus protests against the war or their criticism of the Israeli government.

The administration has also revoked federal funding from universities, including Columbia and the University of Pennsylvania, that it accuses of doing too little to crack down on antisemitism or the participation of transgender women in college sports.

Faiyaz Jaffer, a Muslim chaplain at N.Y.U., said a student discovered the vandalism on Thursday afternoon and rushed to his office to tell him what she had seen. He then notified campus security and university administrators, he said.

“She was in a state of shock, naturally, and I think I was as well,” Dr. Jaffer said, referring to the student. “And then I realized we are kind of used to this. We hear about things like this all the time, but they often go unreported because of a gap between law enforcement and Muslims since 9/11 or because of a distrust people feel toward the authorities.”

Dr. Jaffer called campus security. Word of the vandalism quickly spread among students on social media and WhatsApp.

Safiatu Diagana, 25, a nursing and public health student from Queens, said the incident had left many students feeling hurt and confused. She said she was happy to hear the university say it planned to investigate the vandalism but wanted to see results.

“A lot of us were wondering why — why did this have to happen?” Ms. Diagana said. “We deserve to feel safe on campus, and it is very hurtful and scary that an incident like this can happen here.”

A police spokesman said the vandalism appeared to involve graffiti etched into a wall and written on it in chalk. The spokesman said the department’s Hate Crimes Task Force had been notified and an investigation was underway.

Afaf Nasher, the chairwoman of the New York chapter of the Council on American-Islamic Relations, said the group wanted state and federal law enforcement authorities to open a hate crime investigation into the matter.

“This vile act of desecration is a direct assault on the Muslim community at N.Y.U. and beyond,” she said. “For any student to walk into their prayer space — a sacred space — only to find it defiled, is deeply disturbing.”

The university’s Islamic Center, which provides services and support for Muslim students, said the vandalism was especially disturbing coming so close to Ramadan, which ended last weekend. Center officials said in a statement that the episode was part of a larger tide of anti-Muslim sentiment in the United States.

“This incident is not isolated,” the statement said. “Many in our Muslim community have endured increasing Islamophobia and anti-Muslim rhetoric in recent years. What happened in our prayer space reflects the broader discrimination and challenges Muslims face nationwide.”